# [cig-commits] r8121 - doc/CitcomS/manual

sue at geodynamics.org sue at geodynamics.org
Tue Oct 16 14:55:11 PDT 2007

Author: sue
Date: 2007-10-16 14:55:11 -0700 (Tue, 16 Oct 2007)
New Revision: 8121

Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
typos fixed and wording improved

Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx	2007-10-16 19:06:34 UTC (rev 8120)
+++ doc/CitcomS/manual/citcoms.lyx	2007-10-16 21:55:11 UTC (rev 8121)
@@ -7902,7 +7902,7 @@
initial temperature (1), the number of nodal lines of the perturbation
in the longitudinal direction, e.g., the spherical harmonic order (3), the
number of nodal lines in the latitudinal direction, e.g., the spherical harmonic
- degree (2), which layer the pertubation is on (5), and the amplitude of
+ degree (2), which layer the perturbation is on (5), and the amplitude of
the perturbation (0.05).
Note that although the number of perturbations is assigned here as
\family typewriter
@@ -9872,7 +9872,7 @@
\begin_layout Standard
This example is a benchmark problem for compressible thermal convection.
The Stokes solver in CitcomS has been benchmarked and validated against
- semi-analytical solution.
+ a semi-analytical solution.
However, no analytical solution exists for the benchmark on the energy
equation solver, which is nonlinear.
The steady-state solution is usually used for the comparison with other
@@ -9885,9 +9885,9 @@
\end_layout

\begin_layout Standard
-This cookbook example will run for 10000 time steps to reach steady state.
+This cookbook example will run for 10,000 time steps to reach steady state.
It will use 12 processors and take 1 to 2 days to finish on a modern computer.
- At every 1000th time-step interval, a checkpoint for the internal state
+ At every 1,000th time-step interval, a checkpoint for the internal state
of the solver is saved.
\end_layout

@@ -9898,11 +9898,11 @@
\begin_layout Standard
If the solver is interrupted before finishing the computation, one can resume
the computation from the checkpointed state.
- To shorten the computation time, a checkpoint at the 9000th time step is
- provided.
+ To shorten the computation time, a checkpoint at the 9,000th time step
+ is provided.
(Note that the checkpoint files are produced by a x86 machine and may not
be usable by other types of machines, e.g., PowerPC.) To resume the computation
- from the 9000th time-step checkpoint, set these parameters:
+ from the 9,000th time-step checkpoint, set these parameters:
\end_layout

\begin_layout LyX-Code
@@ -9972,7 +9972,7 @@
\begin_layout Standard
The initial temperature is a conductive profile with a single spherical
harmonic perturbation.
- The pertubation is located at the mid-depth and is defined as:
+ The perturbation is located at the mid-depth and is defined as:
\begin_inset Formula $mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)$

@@ -10198,8 +10198,13 @@
remove_rigid_rotation = on
\end_layout

-\begin_layout LyX-Code
-
+\begin_layout Standard
+However, for models with imposed plate velocity, it is advised to turn off
+
+\family typewriter
+remove_rigid_rotation
+\family default
+.
\end_layout

\begin_layout Subsubsection
@@ -10430,7 +10435,7 @@
\end_inset

.
- A tetrahedra symetric pattern is developed for the convection.
+ A tetrahedra symmetric pattern is developed for the convection.
The surface heatflux
\begin_inset Formula $Q_{surf}$
\end_inset
@@ -10452,12 +10457,13 @@
placement H
wide false
sideways false
-status collapsed
+status open

\begin_layout Standard
\align center
\begin_inset Graphics
filename graphics/cookbook8.png
+	scale 75

\end_inset

@@ -10473,7 +10479,7 @@

\end_inset

-Cookbook 8: The steady state temperature field at the 10000 time step.
+Cookbook 8: The steady state temperature field at the 10,000th time step.
A tetrahedra symmetric convection pattern is developed.
Two temperature isosurfaces of 0.4 and 0.8 are shown.

@@ -10505,7 +10511,7 @@
On the other hand, the plume must be sufficiently away from the sidewalls
to avoid possible boundary effects.
Satisfying both requirements in a model will take a long computation time.
- Using solver coupling, a high-sesolution model with a smaller domain can
+ Using solver coupling, a high-resolution model with a smaller domain can
be nested within a low-resolution model, and the computation time is significan
tly reduced.

@@ -10517,7 +10523,7 @@

\begin_layout Standard
You will use two solvers in the model.
- A special command line option is required for a coupled model.
+ A special command-line option is required for a coupled model.
Typing the following command to run this cookbook example:
\end_layout

@@ -10528,8 +10534,8 @@
\begin_layout Standard
The embeded solver (esolver) is nested within the domain of the containing
solver (csolver).
- Both solvers are instances of a regional CitcomS solver.
- The containing solver can be a full CitcomS solver.
+ Both solvers are instances of a regional CitComS solver.
+ The containing solver can be a full CitComS solver.
\end_layout

\begin_layout LyX-Code
@@ -10564,7 +10570,7 @@

\end_inset

- and is briefly described in the followings:
+ and is only briefly described here:
\end_layout

\begin_layout Enumerate
@@ -10587,8 +10593,7 @@
\begin_inset Formula $dt_{e}$
\end_inset

-.
-
+;
\begin_inset Formula $dt_{e}$
\end_inset

@@ -10600,11 +10605,11 @@
\end_layout

\begin_layout Enumerate
-Goto step 3 until the sum of
+Step 3 is repeated until the sum of
\begin_inset Formula $dt_{e}$
\end_inset

- equal to
+ is equal to
\begin_inset Formula $dt_{c}$
\end_inset

@@ -10620,8 +10625,8 @@
\family typewriter
on
\family default
-), the containing solver updates its temperature according to embedded solver's
- temperature.
+), the containing solver updates its temperature according to the embedded
+ solver's temperature.
\end_layout

\begin_layout Enumerate
@@ -10633,19 +10638,20 @@
\end_layout

\begin_layout Enumerate
-Goto step 1.
+The entire process beginning at step 1 is repeated.
\end_layout

\begin_layout Standard
-The two solver processes are seperated and only communicate through the
- couplers, which, in turn, use the exchanger package to pass messages.
- The containging coupler and controller (ccoupler and ccontroller) are associate
-d with the csolver, and the embedded coupler and controller (ecoupler and
+The two solver processes are separated and only communicate through the
+ couplers, which in turn use the exchanger package to pass messages.
+ The containing coupler and controller (ccoupler and ccontroller) are associated
+ with the csolver, and the embedded coupler and controller (ecoupler and
econtroller) with the esolver.
Each of the two solvers will track its own number of time steps.
The esolver is have a smaller time step size and, hence, a larger number
of time steps.
- The model will finish when either of the solver reach the 200th time step.
+ The model will finish when either of the solvers reaches the 200th time
+ step.
The csolver will output for every 2 steps and the esolver for every 10
steps.
\end_layout
@@ -10670,10 +10676,10 @@
\end_layout

\begin_layout Standard
-A few parameters must be indentical for the ccoupler and ecoupler.
- You will use two-way communication, which enable ecoupler to send temperature
- information to the ccoupler.
- Otherwise, the communication is one way, ccoupler to ecoupler, only, and
+A few parameters must be identical for the ccoupler and ecoupler.
+ You will use two-way communication, which enables the ecoupler to send
+ temperature information to the ccoupler.
+ Otherwise the communication is one way, ccoupler to ecoupler only, and
the csolver is not affected by the esolver.
\end_layout

@@ -10683,9 +10689,9 @@

\begin_layout Standard
There is an option to exchange initial temperature, which could ensure that
- the initial temperature field of both solvers are consistent.
- The initial temperature field will be read from velo files, which already
- contain consistent temperture fields, and don't need to exchange again.
+ the initial temperature field of both solvers is consistent.
+ The initial temperature field is read from velo files, which already contain
+ consistent temperture fields, and don't need to exchange again.

\end_layout

@@ -10708,8 +10714,8 @@
\end_layout

\begin_layout Standard
-The velocity boundadry conditions of esolver is fixed normal velocity and
- shear stress, whose values are received from the esolver.
+The velocity boundary conditions of the esolver are fixed normal velocity
+ and shear stress, whose values are received from the esolver.
Without turning on
\family typewriter
side_sbcs
@@ -10725,8 +10731,8 @@

\begin_layout Standard
Plate motion is imposed on top of the esolver, which has a mid-ocean ridge
- with a 5 cm/yer half spreading rate.
- A transfrom fault cuts through the ridge.
+ with a 5 cm/year half-spreading rate.
+ A transform fault cuts through the ridge.
Setting
\family typewriter
start_age
@@ -10757,20 +10763,43 @@

\begin_layout Standard
The domain of the csolver is bigger than that of the esolver.
- The radial dimension of esolver is shrank slightly with repect to csolver
- so that the domain of esolver is completely inside the domain of csolver.
- The radial coordinate of csolver is refined near the top and bottom boundary
- (
+ The radial dimension of the esolver will shrink slightly with respect to
+ the csolver so that the domain of the esolver is completely inside the
+ domain of the csolver.
+ The radial coordinate of the csolver is refined near the top and bottom
+ boundaries (
\family typewriter
coor=2
\family default
-), with the lower 10% of the mesh divided by 15% of nodes, upper 10% of
- the mesh divided by 20% of nodes, and the rest 80% of the mesh divided
- by 75% of nodes.
- Be cautious that if the mesh size changes too rapidly across a element,
- the temperature solver might generate pronouncing numerical artifact.
+), with the lower 10% of the mesh divided by 15% of the nodes, the upper
+ 10% of the mesh divided by 20% of the nodes, and the remaining 80% of the
+ mesh divided by 75% of the nodes.
+
\end_layout

+\begin_layout Standard
+Therefore, when setting the values of
+\family typewriter
+coor_refine
+\family default
+ (see below), be careful not to set the first or third value (in example
+ below,
+\family typewriter
+ 0.1
+\family default
+) too low, or the second or fourth value (in example below,
+\family typewriter
+0.15
+\family default
+ and
+\family typewriter
+0.2
+\family default
+) too high.
+ This can cause the mesh size to change too rapidly across an element and
+ the temperature solver to generate pronounced numerical artifacts.
+\end_layout
+
\begin_layout LyX-Code
[CitcomS.csolver.mesher]
\newline
@@ -10834,26 +10863,26 @@
\family default
).
- A Lenardic-type filter, which removes numerical artifact while keeping
+ A Lenardic-type filter, which removes numerical artifacts while keeping
total energy conserved, is disabled (
\family typewriter
filter_temp
\family default
).
- The maximum temperature can be monitor between time steps (
+ The maximum temperature can be monitored between time steps (
\family typewriter
monitor_max_T
\family default
).
If the maximum temperature increases too much (> 5%) between time steps,
- the temperature solve will rerun with half time step size.
- The time step size is usually determined dynamically according Courant
+ the temperature solver will rerun with half time-step size.
+ The time-step size is usually determined dynamically according to Courant
criterion and is reduced by a fraction (
\family typewriter
finetunedt
\family default
-) to improve the accuracy.
- The time step size can also be specified staticly in
+) to improve accuracy.
+ The time-step size can also be specified statically in
\family typewriter
fixed_timestep
\family default
@@ -10862,7 +10891,7 @@
fixed_timestep
\family default
is non-zero.
- The temperature solver uses a explicitly predictor-corrector algorithm.
+ The temperature solver uses an explicitly predictor-corrector algorithm.
Using 0.5 for the predictor (
\family typewriter
@@ -10871,7 +10900,7 @@
\family typewriter
\family default
-), this algorithm is 2nd order accurate.
+), this algorithm is second-order accurate.
\end_layout

\begin_layout LyX-Code
@@ -11243,7 +11272,7 @@
\end_layout

\begin_layout Standard
-The results for this problem are presented in Figure
+The solution of this problem is presented in Figure
\begin_inset LatexCommand ref
reference "fig:Cookbook-9"

@@ -11253,8 +11282,8 @@
The plume head spreads below the lithosphere, and the plume conduit is
elongated in the ridge-parallel direction.
The lithosphere subducts at the left and right edges of the csolver.
- The domain of csolver could have been bigger so that the plume could be
- further away from the subducted slabs.
+ If the domain of the csolver were bigger, the plume would be further away
+ from the subducted slabs.

\end_layout

@@ -11268,7 +11297,8 @@
\begin_layout Standard
\align center
\begin_inset Graphics
-	filename /Users/tan2/cig/doc/CitcomS/manual/graphics/cookbook9.png
+	filename graphics/cookbook9.png
+	scale 60

\end_inset

@@ -11287,8 +11317,8 @@
Cookbook 9: The plume head spreads below the lithosphere, and the plume
conduit is elongated in the ridge-parallel direction.
The temperature isosurface is at 0.8.
- The grid spacings of both meshes are reduced approximately three-folds
- for better visualization.
+ The grid spacings of both meshes are reduced approximately threefold for
+ better visualization.
\end_layout

\end_inset